Liam Research 1

GSE129166

# gse129166 <- getGEO("GSE129166")
Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 2)
gse <- getGEO(filename="Data/GSE129166_series_matrix.txt.gz")

Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpO2Degc/GPL570.soft.gz 

gse

ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 212 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM3701699 GSM3701700 ... GSM3701910 (212 total)
  varLabels: title geo_accession ... tissue:ch1 (41 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 31378695 
Annotation: GPL570 

fData(gse)

pData(gse)

data.frame(exprs(gse))

#GSE34748

#gse34748 <- getGEO("GSE34748") # Then go to file loc and move downloaded file to data folder

Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 2)
gse <- getGEO(filename="Data/GSE34748_series_matrix.txt.gz")

Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpO2Degc/GPL570.soft.gz 

gse

ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 56 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM854492 GSM854493 ... GSM854547 (56 total)
  varLabels: title geo_accession ... tissue:ch1 (32 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 22335458 
Annotation: GPL570 

fData(gse)

pData(gse)

data.frame(exprs(gse))

getGEO("GSE51675")

Found 1 file(s)
GSE51675_series_matrix.txt.gz

$GSE51675_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 41093 features, 18 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM1250391 GSM1250392 ... GSM1250408 (18 total)
  varLabels: title geo_accession ... treatment:ch1 (41 total)
  varMetadata: labelDescription
featureData
  featureNames: (+)E1A_r60_1 (+)E1A_r60_3 ... RC9 (41093 total)
  fvarLabels: ID SPOT_ID ... SEQUENCE (17 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 25925804 
Annotation: GPL6480 

getGEO("GSE343")

Found 2 file(s)
GSE343-GPL271_series_matrix.txt.gz
GSE343-GPL272_series_matrix.txt.gz

$`GSE343-GPL271_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 28032 features, 66 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM4776 GSM4777 ... GSM4841 (66 total)
  varLabels: title geo_accession ... data_row_count (43 total)
  varMetadata: labelDescription
featureData
  featureNames: 1 2 ... 28784 (28032 total)
  fvarLabels: ID NAME ... SPOT_ID (21 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 12853585 
Annotation: GPL271 

$`GSE343-GPL272_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 37632 features, 1 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM4842
  varLabels: title geo_accession ... data_row_count (43 total)
  varMetadata: labelDescription
featureData
  featureNames: 1 2 ... 37632 (37632 total)
  fvarLabels: ID NAME ... LUID (20 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 12853585 
Annotation: GPL272 

getGEO("GSE15296")

Found 1 file(s)
GSE15296_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpO2Degc/GPL570.soft.gz 

$GSE15296_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 75 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM382248 GSM382249 ... GSM382322 (75 total)
  varLabels: title geo_accession ... tissue:ch1 (38 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 24725967 
Annotation: GPL570 

getGEO("GSE46474")

Found 1 file(s)
GSE46474_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpO2Degc/GPL570.soft.gz 

$GSE46474_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54613 features, 40 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM1130812 GSM1130813 ... GSM1130851 (40 total)
  varLabels: title geo_accession ... tissue:ch1 (46 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... 91952_at (54613 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 25387159 
Annotation: GPL570 

getGEO("GSE50084")

Found 1 file(s)
GSE50084_series_matrix.txt.gz

$GSE50084_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 29096 features, 115 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM1213867 GSM1213868 ... GSM1213981 (115 total)
  varLabels: title geo_accession ... tissue:ch1 (32 total)
  varMetadata: labelDescription
featureData
  featureNames: 7896736 7896738 ... 8180418 (29096 total)
  fvarLabels: ID GB_LIST ... category (12 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 26484130 
Annotation: GPL6244